[2023-06-13 09:12:08,033] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:12:08,037] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:12:08,037] [INFO] DQC Reference Directory: /var/lib/cwl/stg03880cda-c46f-4e04-ae64-60507536b258/dqc_reference
[2023-06-13 09:12:09,249] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:12:09,250] [INFO] Task started: Prodigal
[2023-06-13 09:12:09,250] [INFO] Running command: gunzip -c /var/lib/cwl/stga825ce1b-9c3d-4702-aca1-6623ff091807/GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:12:13,028] [INFO] Task succeeded: Prodigal
[2023-06-13 09:12:13,029] [INFO] Task started: HMMsearch
[2023-06-13 09:12:13,029] [INFO] Running command: hmmsearch --tblout GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03880cda-c46f-4e04-ae64-60507536b258/dqc_reference/reference_markers.hmm GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:12:13,261] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:12:13,264] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga825ce1b-9c3d-4702-aca1-6623ff091807/GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-13 09:12:13,312] [INFO] Query marker FASTA was written to GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 09:12:13,313] [INFO] Task started: Blastn
[2023-06-13 09:12:13,313] [INFO] Running command: blastn -query GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg03880cda-c46f-4e04-ae64-60507536b258/dqc_reference/reference_markers.fasta -out GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:12:13,886] [INFO] Task succeeded: Blastn
[2023-06-13 09:12:13,889] [INFO] Selected 10 target genomes.
[2023-06-13 09:12:13,890] [INFO] Target genome list was writen to GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 09:12:13,892] [INFO] Task started: fastANI
[2023-06-13 09:12:13,892] [INFO] Running command: fastANI --query /var/lib/cwl/stga825ce1b-9c3d-4702-aca1-6623ff091807/GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:12:19,332] [INFO] Task succeeded: fastANI
[2023-06-13 09:12:19,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03880cda-c46f-4e04-ae64-60507536b258/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:12:19,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03880cda-c46f-4e04-ae64-60507536b258/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:12:19,337] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 09:12:19,337] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 09:12:19,337] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Ruminococcus flavefaciens	strain=ATCC 19208	GCA_000518765.1	1265	1265	suspected-type	True	77.6553	89	521	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 09:12:19,339] [INFO] DFAST Taxonomy check result was written to GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 09:12:19,340] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:12:19,340] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:12:19,340] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03880cda-c46f-4e04-ae64-60507536b258/dqc_reference/checkm_data
[2023-06-13 09:12:19,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:12:19,367] [INFO] Task started: CheckM
[2023-06-13 09:12:19,367] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 09:12:37,501] [INFO] Task succeeded: CheckM
[2023-06-13 09:12:37,502] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:12:37,518] [INFO] ===== Completeness check finished =====
[2023-06-13 09:12:37,519] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:12:37,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 09:12:37,519] [INFO] Task started: Blastn
[2023-06-13 09:12:37,519] [INFO] Running command: blastn -query GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg03880cda-c46f-4e04-ae64-60507536b258/dqc_reference/reference_markers_gtdb.fasta -out GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:12:38,308] [INFO] Task succeeded: Blastn
[2023-06-13 09:12:38,314] [INFO] Selected 14 target genomes.
[2023-06-13 09:12:38,314] [INFO] Target genome list was writen to GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:12:38,319] [INFO] Task started: fastANI
[2023-06-13 09:12:38,319] [INFO] Running command: fastANI --query /var/lib/cwl/stga825ce1b-9c3d-4702-aca1-6623ff091807/GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:12:43,974] [INFO] Task succeeded: fastANI
[2023-06-13 09:12:43,985] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 09:12:43,985] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_009177225.1	s__Ruminococcus sp009177225	94.9582	388	521	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002362175.1	s__Ruminococcus sp002362175	85.8957	370	521	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017622635.1	s__Ruminococcus sp017622635	84.3287	241	521	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014799765.1	s__Ruminococcus sp014799765	79.3007	179	521	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001604035.1	s__Ruminococcus sp001604035	77.8854	75	521	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.76	98.76	0.77	0.77	2	-
GCA_017543595.1	s__Ruminococcus sp017543595	77.8719	142	521	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.43	98.43	0.97	0.97	2	-
GCA_002389995.1	s__Ruminococcus sp002389995	77.5871	115	521	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	96.64	96.54	0.80	0.76	5	-
GCA_017397925.1	s__Ruminococcus sp017397925	77.5262	101	521	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017441505.1	s__Ruminococcus sp017441505	77.3732	84	521	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017543335.1	s__Ruminococcus sp017543335	77.3093	85	521	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.36	98.36	0.90	0.90	2	-
GCA_017513795.1	s__Ruminococcus sp017513795	77.2294	107	521	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.92	97.92	0.90	0.90	2	-
GCA_017418765.1	s__Ruminococcus sp017418765	77.0371	50	521	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902796705.1	s__Ruminococcus flavefaciens_W	76.4327	69	521	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 09:12:43,987] [INFO] GTDB search result was written to GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 09:12:43,988] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:12:43,992] [INFO] DFAST_QC result json was written to GCA_947178545.1_SRR14411261_bin.2_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 09:12:43,992] [INFO] DFAST_QC completed!
[2023-06-13 09:12:43,992] [INFO] Total running time: 0h0m36s